The Start of Something New
by MoniMcCoy
Summary: They both had been too young to know and understand what their parents had planned for them. For Molly it meant making new friends and learning a new culture. For Noonien it meant another addition to the tool of scientists that experimented on him to create the perfect human being. Only this one, came with a daughter in the same package.
1. Chapter 1

**And finally, I put here the first part of what I think it's gonna be three part fanfiction.**

**Leave a review, they encourage me to write more!**

They both had been too young to know and understand what their parents had planned for them. For Molly, the prospect of moving with her father to another research team located in Bombay, India, meant that she had the posibilities of learning a new language, a new culture, meeting new peope, make new friends... For Noonien, that same prospect meant another different thing: that there was going to be another adittion to the tool of scientists that experimented on him to create the 'perfect human being' as they liked to call it.

This one came with a young daughter in the same package, which could only mean he would have to babysit a child, since his father was really interested in them to become good friends, maybe even better friends than him and his fellow British Augment Jonathon. He had complained almost instantly, partially because he disaproved the idea of becoming friends with someone he barely knew, less a girl that was at least three years younger than him.

Now that he had her in front of him, the only thing he could think about was how much he hated that stupid girl, with her too big eyes, her too skinny legs , her too pale skin and her too cute blush that perfectly matched the soft pinkness of her thin lips..

Shaking those thoughts from his head he reluctantly grabbed her small hand in his, marvelling the softness of her porcelain skin for a second before pulling her roughly towards him and striding towards the main halls of the scientific base, hoping that during that long tour she would show her true annoying nature and leave him alone.

However, it only got worse for him. She was polite, sweet and only spoke when she was spoken to. She was 'Little Miss Perfect' as Noonien liked to call her on his head. Soon, he discovered to his great displeasure that the more time passed, the more he enjoyed her company.

Noonien was just a twelve year old to understand what he was feeling. Nevertheless, his behavior wasn't invisible for their parents. Who as soon as they were left alone, they started talking about compromises and arranged marriages.

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><p>As time passed, he made some new discoveries about her. She wasn't like the other girls he knew. Apart from the fact that she was entirely human, she wasn't as annoying and aggresive as the others (with the exception of the American Augment Marie, a close friend of Jonathon who was the less annoying Augment female but no less aggresive). She just sat on a corner, reading a book and staying quiet until her father called for her. When his training and experiment session ended, Noonien always sat at the other end of the room watching her intently. Sometimes when she read, she smiled, a soft small smile that he didn't know why, but he never wanted to loose sight of it. Marie always liked to tease him about it saying that if he continued o look at her like that, the experiments would finally succeed and he would shot rays through his eyes.<p>

It wasn't until much later that Noonien was brave enough to approach her, however he felt like he didn't make the best of the impressions.

She had been reading as always, she seemed so immersed in her story that she didn't notice the angry looking Augment boy approaching her. But Noonien did, and as soon as the boy dared to talk her he was already standing up and getting ready for battle.

"You, give me that book." The boy spoke harshly. Molly looked up, wide-eyed and probably scared of the taller boy. She clutched the book to her chest, refusing to give it to that brute of a kid. That seemed to anger more the young Augment.

"Are you deaf? Give me that book!" The boy shouted, lifting his arm to get the book using brute force.

Molly shivered and shrunk into herself, awaiting the imminent punch. But it never came. Instead a cry of pain and the sound a bone breaking was heard. She looked up and saw Noonien twisting the other boy's arm behind his back, though it wasn't necessary anymore. The boy's arm was completely broken, as the bone could be seen peering through the skin. Also, he seemed to be sporting a very bad looking bloody nose.

"Listen to me, you filthy scum. If I ever see you talking to her or just standing near her again, I'll rip all your limbs from your body, starting with the most precious to you." Noonien hissed at the ear of his adversary, signaling with his head the area where his crotch was positioned. The young Aument just nodded and ran away from him when he was released from Noonien's deadly grasp. Watching him go, Noonien wondered why he hadn't killed him as he did years ago wih that Augment bully who wanted to take his so needed crutch from him. He had a vague idea of who could be the one to blame for his 'gentelmanly' behavior, and she was sitting just behind him, probably with an amazed and fearful look in her eyes.

"Are you okay?." He asked curtly, . She looked at him with a smile, he noted that her eyes were brighter when she smiled, at least when she smiled at him.

"Yes, thanks Noonien." His name was pronounced as if it was the sweetest of the sweets. Noonien wasn't sure if it should bother or please him, he had been told he should be respected after all, not loved.

"What were you reading?" He demanded. One of the few things that bothered him about her was that he was never certain about what to say to her that could really catch her attention, and he highly doubted she was interested in hearing about his experiments and training lessons. But books seemed a good topic, so why not?

"Just a history book that my mother gave me when I was young. She really loved history." She answered shyly, lowering her gaze. That was another of the few things about her that really bothered Noonien. Sometimes, she seemed willing to talk to him as if he was an old friend, but then she would refuse to look at his eyes and act like if they had just met and she feared his opinion about her. Something snapped on Noonien's head, this time he wasn't going to allow that to happen. He crouched at her level and forced her to look at him.

"What was your mother's name?" He asked, really insterested on her answer.

"Marla. She died when I was young." Molly said with sad eyes. Noonien felt a pinch of sympathy for the girl, as he had also lost his mother at a really young age. Although in his case, he had been to young to have any memories of her, he could imagine how hard must have been for Molly to lose someone as important as her mother.

"I'm sorry." He said without thinking. Later, he would be surprised about how someone as proud and stoic as him could have apologized for something to someone as meek and quiet as her. At first, he thought she had hacked his neural chip to make him more emotional and therefore weaker. But when he asked his 'father' to take a look at it and he said that it was as good as new, Noonien started to worry about how much power could have that small girl over him.

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><p>That power, he unfortunately discovered , it was really strong, so strong that even her absence raged at him. Molly was a constant on his life, and although she was quiet and almost invisible constant, you could easily tell when she was missing.<p>

That day she had been on a nearest town on a shopping trip with her father, and not even two hours had passed before Noonien found himself missing, because craving and needing just sounded too pathetic for him, her company.

That day, not even his constant experiments on himself, like how many and how serious injures he could take, that usually ended with him on the infirmary with Molly, Johnathon and Marie at his side, could cheer him up.

However, as he thought about it, he questioned himself why he couldn't go with her to the town, why couldn't he go anywhere at all? Why did they want to keep him caged? To keep _them _caged? Noonien found it quite unfair, and soon found himself wondering about different ways of escaping without getting caught. Soon he came to a simple conclusion: the key were the cameras and that monitoring sistem that were implanted in every room and laboratory of the base. But those were easy to disable, the problem was the many guards that guarded the exits.

Noonien knew that he was stronger than any other boy, Augment or human, it didn't matter; but face all those guards was out of the question. His main goal was to not to be seen or heard and a fight would only complicate things. So he opted to dig a hole on the computer room that would lead him towards his freedom. Once again, the doctors would be atonished with his strenght as they had believed that stone floor to be nearly impossible to break.

When his face peered through the burning sand of the desert, he swore he had never felt more alive in all his life. It's a shame that his happiness only lasted a few seconds, because when he was able to pull his entire body of the hole a sharp pain on the back of his head make him fall on his kees. It hurted, as his head was exploding over and over again, his self inflicted wounds on training sessions were reduced to nothing compared to this. Why did he have to suffer so much? He just had wanted to see Molly, nothing more.

From a nearby helicopter a man looked with pain in his eyes how the neural chip worked its magic on the boy he had 'created', the boy he had come to love as his own child.

"I'm sorry, Noonien." said. "But I don't think the world is ready for you yet."

Noonien learnt his lesson, though the idea of escaping remained on his head. The next time, he would be more careful and he would make sure to not get caught again.

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><p>At the complex age of fifteen Noonien asked Molly to lend him the history book that her mother had given her to read it. Just for curiosity, and knowledge, at least that was he said to her and himself. Though he couldn't help but feeling a bit of smugness at the thought of her trusting him enough to lend him one of her most treasured possessions.<p>

He had planned to read the book later, at night. But the curiosity of discovering what could be written on that book for the deceased Marla Hooper to give it to her daughter won and he barely made it to his room when he opened the book and started reading.

To say he was amazed with all that ancient conquerors and warriors was an understatement. He was marvelled by them, and he couldn't help but feel a bit reflected on them. He was also a warrior, he had been trained to fight, to develop his skills. One day, he hoped it was sooner than later, he would have to fight along his comrades in wars and battles, he would be a great warrior and a military leader. Just like Gengis Khan.

_Khan._ He found he really liked the name, it sounded powerful, strong and royal, Hell, even it's meaning was _king_, and now that he thought about it, it suited him. He wasn't the strongest, cleverest and fastest of all his generation for nothing.

He returned the book to Molly a few weeks later, with a small smile on his face, which given who he was and his backstory, it was like he was beaming with happiness.

"Did you enjoy the book?" She asked, amused that her friend was finally showing some facial expressions. Noonien kept the smile on his face.

"Of course, it was a quite intersting subject. One can be really surprised at all the things that our ancestors did, no wonder why you read it so much, it's fascinating."

Molly was the one beaming now at the fact that he had liked the book.

"Although I'm more interested in medicine and anatomy, I agree that is a great book. I'm glad you liked it, Noonien."

"_Khan."_ He corrected her, his smile widening "My name is _Khan Noonien Singh._"


	2. Chapter 2

**Hi! Sorry it took so long for me to update, but many things had happened: I had to do projects, I had to spend Christmas without wifi, I had to take care of the mess my rabbit made because he got diarrhea... twice, and now I have to study for the finals because I don't know how it is in the rest of the world, but here in Spain we have the final exams in January :( Anyway, here it is at last, though I planning to add one more chapter to the original three.**

**Enjoy!**

Noonien, now known as Khan had just turned eighteen when his creator and Molly's father talked him about the plans Dr. Hooper and him had for both him and Molly. He had been choleric, fuming with rage and and had destroyed nearly everything he found on his path. How dared they?

As not many would have thought he wasn't entirely opposed to the thought of being engaged to Molly, lately he had come to notice and appreaciate the quite impressive changes that puberty had made on her. It was the thought of those doctors planning his and Molly's life what stirred his blood.

He was his own person, who made his own decisions, and if Molly and him ended togheter would be because he had proposed to her, not because someone had forced them. Still, the thought of Molly belonging to him was really appealing, though he would have to wait some years until she was of legal age to marry him.

"Best start the courting phase now, then" He mused, having already forgiven the doctors for their small slip. But, although he had forgiven them, that didn't mean he had forgotten. Because Khan never forgot insolences like that.

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><p>When Molly was sixteen, her father had died after a long and hard fight with cancer, and had left her alone with Dr. Heisen as her legal guardian and without the knowledge of what they had planned for her and Khan when she turned eighteen.<p>

And Khan wanted it to remain a secret. He didn't want her to feel forced when he proposed, because he was going to propose to her, he had long decided that he wanted to keep her by his side as he found her terribly interesting and had developed a great affection for her, that he would never call love because _love_ didn't exist.

However that affection was enough to make a wave of protectiviness rush over him when he saw her crying in front of the corpse of her father. That moment he vowed to himself to destroy everything that made her feel as sad as that.

The next time he saw her, she had been sitting on her father's bed, facing the walll. Khan had approached her and had embraced as tightly as he could without crushing all the bones in her body. She was shaking, because the sobs that rushed through her body, and didn't seem to stop any soon. So he opted for the unthinkable, at least for her: he kissed her on the lips.

When his full lips crashed against her small soft ones, her first reaction was to still herself; but soon with a few encouraging pushes of his lips, she melted on their passionate snog.

When his hands descended to her hips, she abruptly ended de kiss, leaving him cold and confused. "Why did you do that?" She asked dumbfonded.

"I just try to make you feel better, I'm not doing it good?"

Molly's ears, cheeks and neck reddened, and Khan wondered how far would that blush go.

"Y-yes you are d-doing it g-good." She took a deep breath to stop stammering. "I just thought you didn't see me like that."

"And why wouldn't I see you like that?" He purred on her ear, enjoying the shiver that ran through her petite body. Molly felt her mind cloud and her eyelids beginning to close in a haze of pleasure.

"Answer me, Molly." He nibbled on her ear lobe and deposited small kisses from her jaw to her chin. This time Molly lifted her head and pressed her lips to his, their tongues battling for dominance. Khan, refusing to let her win this round took the lead and pressed her against the wall, and then against the bed, where they settled the base of a new relationship.

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><p>"I want to go to University."<p>

Six words. It only took her six words to destroy all of Khan's planning and schemes. Why did she want to go when she knew he couldn't leave, at least not yet? Why leave him and everything they had?

"But why Molly?" He said, taking care of his tone of voice. Khan Noonien Singh did never sulk.

Molly sighed and sat in front of him.

"It's just that since my father died, I've never been able to go out or do many things than to stay there with the scientifics. And I want to do something with my life."

Khan knew that once she put her head into something, there was nothing that would convince her otherwise. She was just so bloody stubborn. Just like him. Maybe he could convince her to study in a town next to the base.

"And where would you like to study?" He asked pretending to be as accepting and considerate as any other boyfriend.

"London."

"What!?"

* * *

><p>She was gone. And with her had gone his patience, his compassion and his politeness. Not even a week had passed before he found himself hot and hard again for her touch, for her lips kissing his tanned shoulders, and her soft moans everytime he made her his. Khan wasn't just an horny teenager, he was an horny angered augmented teenager.<p>

As time passed, he found himself growing more irascible and irritated. He needed to get out, he needed to see her. What if she was scared? What if she was attacked? What if any of that pompous english boys dared to touch her? Khan dented the metal wall with a punch.

He had to get out.

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><p>Dr. Heisen ran through the halls of the base. Where was everyone? Where did the other scientists and guards go? Where were the Augments? Dr. Heisen was fearing the worst, so he opted for going to the only place he could think about: The training yard. What he saw there, made his heart stop and his blood run cold.<p>

His colleages, his friends, his fellows; they all lay sprawled through the sandy soil, wounds and cuts and limbs turned in weird angles decorating their bodies. They were all dead. And in the middle of everything, the Augment teens, _his children_, stood proud over the slaughtering.

"Khan! What does this mean?"

Khan just looked at him coldly and extended his arm, to give the man a red box.

"Dr. Heisen, this is for you, to celebrate the importance of this day."

Dr. Heisen hesitantly opened the box, and when he saw its contents he wished he hadn't done so.

"Those are... your neural chips." He said with a light tremor on his voice. Khan felt the strong urge to smirk cruelly at him, but he managed to keep an impassive face. He was a liar, and a traitor; but he had been his, _their _father.

"It's a shame you won't live enough to see the results of your creations "

With his big hands, he grabbed each side of Heisen's head and tightened his grip until there wasn't more than a mass of blood and brain matter covering his hands. He let him, or whatever was left of him, go, repulsed at the mere side of it. Not because the blood and crushed bones, he found quite estimulating to see that he had the strenght to easily crush a human skull; but because the man who had previously been the owner of that skull. He turned towards his brothers and sisters.

"My fellow Augments, there's a whole new world waiting for us, _shall we begin?_

As he stood over the corpse of whom he had once wrongly thought to be his 'father' and 'mentor', he vowed to himself that Molly would never know about that act of brutality.

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><p>He had been impatient to see her, he could barely contain his emotions when he stepped in which he thought was her residency. It was a simple, ugly and depressive gray block with tiny rooms on the inside. Khan looked at it with disgust, he could give his Molly so much more. If that bicyle boy's information was correct her room was on the third floor, third door at the left.<p>

He knocked on the door and waited, his superior hearing listenting to his Molly giving a sigh of desperation and reeling towards the door.

"What do you want now, Alec?" She asked annoyed, but when she saw who it really was. Her expression changed towards one of surprise.

"Khan?" She asked dumbfounded.

"Who is Alec?" Khan asked back narrowing his eyes, feeling the jealously run through him.

"An asshole from class. Wha-what are you doing here?" She inquired leading him towards her room.

"Aren't you happy to see me?" He purred grabbing her waist and pulling her to him for a hot passionate kiss. While kissing her, he took his chance and trust his pelvis roughly against her tight, just to show her how hard he was for her, making her moan in appreciation. After a few seconds, Molly broke the kiss.

"Of course, I'm happy to see you, love. It's just... How did you managed to escape? And won't be they looking for you right now?" Molly asked worried about what could happen to her boyfriend.

Khan let out a soft chuckle and kissed her cheek.

"They let us go, dear."

Molly frowned. "They let you all... go?"

"Yes." He answered, frowning as well. Molly slowly pulled away from him, uncertainty in her eyes.

"Khan, what happened?" She asked.

"I told you, they let us-"

"They let go more than a hundred genetically engineered teenager to roam freely over the world? Please, tell me the truth. Even you know how bad that lie is."

Khan set his mouth in a tight line, he had hoped she had avoided that part.

"We killed them."

Molly paled and took several steps back, he felt cold without her warm presence at her side.

"W-what? You killed them all?" She said in a whisper.

"We had to. You can't imagine what they had planned for us!" Khan said trying to defend their acts.

"And killing them all was the solution!?" Molly screamed.

"Of course it was! They all deserved to die! Those filthy arrogant scientists who only cared about themselves and their goals should burn in hell! I'm proud of what we did, and I'll be willing to do it again if that means riding them from existence!"

The room was silent for a few seconds after Khan outburst. His dark eyes could see with clarity how his Molly's expression changed from shock to fear, and then to digust, to anger, and last, to sadness.

"My father used to be one of them. Would you have also killed us?" She whispered, her eyes widening with fear at the realisation that he may have been toying with her all this time and was going to kill her now to leave no loose ends.

Khan clenched his fists a sudden feeling of panic growing in his stomach, she was getting everything wrong. She didn't understand their motives, he had to make her see.

"Get out, please." She said turning her head to the side.

He made an attempt to reach for her, to hug her and talk some sense into her. But it wouldn't be welcomed, not when she was still processing all the information. He would have to be patient, even if it hurt both his pride and heart.

* * *

><p>Three months. Three fucking months of waiting under her window every afternoon for her to forgive him and let him explain, and she still hadn't spoken a word to him. But at least those months hadn't been in vain. The Augments had finally managed to infiltrate all of the most powerful goverments of earth, it'll take them months to bring them down and take power, but they'd finally succeed. Of course, he knew they'll succeed, because humans were that guillible, they wouldn't notice what's under their noses even if you point that to them, they were like sheeps that didn't know that they were going to be attacked by wolves. And he was a very hungry wolf.<p>

As much as he had vowed himself to not leave to India without her, he was running out of time, and if he wanted to get some job done, he'll have to leave Molly aside. He had been very patient with her, as strange as it was, but he wasn't going to let her tantrum spoil the mission he and his brothers and sisters had put so much effort in.

He would return to India, and he would continue with their plan. Molly would have to wait for now, but at the end, she'll come to him, as always.

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